Extracting biological information with computational analysis of Fourier-transform infrared (FTIR) biospectroscopy datasets: current practices to future perspectives

Applying Fourier-transform infrared (FTIR) spectroscopy (or related technologies such as Raman spectroscopy) to biological questions (defined as biospectroscopy) is relatively novel. Potential fields of application include cytological, histological and microbial studies. This potentially provides a rapid and non-destructive approach to clinical diagnosis. Its increase in application is primarily a consequence of developing instrumentation along with computational techniques. In the coming decades, biospectroscopy is likely to become a common tool in the screening or diagnostic laboratory, or even in the general practitioner's clinic. Despite many advances in the biological application of FTIR spectroscopy, there remain challenges in sample preparation, instrumentation and data handling. We focus on the latter, where we identify in the reviewed literature, the existence of four main study goals: Pattern Finding; Biomarker Identification; Imaging; and, Diagnosis. These can be grouped into two frameworks: Exploratory; and, Diagnostic. Existing techniques in Quality Control, Pre-processing, Feature Extraction, Clustering, and Classification are critically reviewed. An aspect that is often visited is that of method choice. Based on the state-of-art, we claim that in the near future research should be focused on the challenges of dataset standardization; building information systems; development and validation of data analysis tools; and, technology transfer. A diagnostic case study using a real-world dataset is presented as an illustration. Many of the methods presented in this review are Machine Learning and Statistical techniques that are extendable to other forms of computer-based biomedical analysis, including mass spectrometry and magnetic resonance.     

New para-para stilbenophanes: synthesis by McMurry coupling, conformational analysis and inhibition of tubulin polymerisation

The synthesis of a new family of methoxy-substituted [2.7]- and [2.8]paracyclophanes linked by 3-oxapentamethylene-1,5-dioxy and hexamethylene-1,6-dioxy bridges has been carried out by using the McMurry methodology. Related indole compounds were also synthesised. Olefin-to-diol ratios depended on the bridge length, the structure of the aromatic ring and the reaction conditions. Macrocyclisation, the methoxy substituents and the presence of a rigid indole moiety restricted the conformational equilibria, as observed by NMR spectroscopy and according to theoretical calculations. The synthesised compounds display micromolar tubulin polymerisation inhibitory activity. The conformational implications on the tubulin polymerisation inhibitory activity derived from the macrocyclisation when compared with combretastatins, closely related stilbenes, are also discussed.     

Segregation of human prostate tissues classified high-risk (UK) versus low-risk (India) for adenocarcinoma using Fourier-transform infrared or Raman microspectroscopy coupled with discriminant analysis

Vibrational spectroscopy techniques can be applied to identify a susceptibility-to-adenocarcinoma biochemical signature. A sevenfold difference in incidence of prostate adenocarcinoma (CaP) remains apparent amongst populations of low- (e.g. India) compared with high-risk (e.g. UK) regions, with migrant studies implicating environmental and/or lifestyle/dietary causative factors. This study set out to determine the biospectroscopy-derived spectral differences between risk-associated cohorts to CaP. Benign prostate tissues were obtained using transurethral resection from high-risk (n = 11, UK) and low-risk (n = 14, India) cohorts. Samples were analysed using attenuated total reflection Fourier-transform infrared (FTIR) spectroscopy, FTIR microspectroscopy and Raman microspectroscopy. Spectra were subsequently processed within the biochemical cell region (1,800⁻¹–500 cm^–1) employing principal component analysis (PCA) and linear discriminant analysis (LDA) to determine whether wavenumber–absorbance/intensity relationships might reveal biochemical differences associated with region-specific susceptibility to CaP. PCA-LDA scores and corresponding cluster vector plots identified pivotal segregating biomarkers as 1,582 cm⁻¹ (Amide I/II trough); 1,551 cm⁻¹ (Amide II); 1,667 cm⁻¹ (Amide I); 1,080 cm⁻¹ (DNA/RNA); 1,541 cm⁻¹ (Amide II); 1,468 cm⁻¹ (protein); 1,232 cm⁻¹ (DNA); 1,003 cm⁻¹ (phenylalanine); 1,632 cm⁻¹ [right-hand side (RHS) Amide I] for glandular epithelium (P < 0.0001) and 1,663 cm⁻¹ (Amide I); 1,624 cm⁻¹ (RHS Amide I); 1,126 cm⁻¹ (RNA); 1,761, 1,782, 1,497 cm⁻¹ (RHS Amide II); 1,003 cm⁻¹ (phenylalanine); and 1,624 cm⁻¹ (RHS Amide I) for adjacent stroma (P < 0.0001). Primarily protein secondary structure variations were biomolecular markers responsible for cohort segregation with DNA alterations exclusively located in the glandular epithelial layers. These biochemical differences may lend vital insights into the aetiology of CaP.     

Charged pion production in 70 GeV/cK + p interactions

Inclusive charged pion production is studied in an exposure of BEBC, filled with hydrogen, to an incidentK ⁺ beam of 70 GeV/c. Total cross sections for pion production and inclusive longitudinal and transverse momentum distributions of π^?'s and of positive particles are presented and compared with data at lower energies. Earlier evidence for scaling in the fragmentation regions is confirmed. The central region π^? cross section increases proportionally top _LAB ^?1/4 ; positive particles show almost no energy dependence atx=0. Particle ratios π⁺/π^? are studied as a function ofx andy ^* and a comparison with 70 GeV/cK ^? p data is made. Analysis of structure functions for (ππ) pairs and of particle production associated with π^± triggers at large |x| in the context of quark/parton models, provides qualitative evidence for the diquark-quark structure of the proton.     

Evaluation of crude oil oxidation by accelerating rate calorimetry

Accelerating rate calorimetry has been used to study the thermal behavior of the combustion reactions that occur during the in situ combustion process and to estimate key parameters for the numerical simulation studies. This work reports the results from a study on the combustion reactions of heavy oil based on experimental tests using an accelerating rate calorimeter. The temperature settings covered a ramped ranging from 50 to 550 °C. The pressure was kept constant at 20 and 40 bar, and the air flow rates were tested for values of 90 and 120 mL min^?1. An experimental design was built to provide the effects of pressure, air inflow, and oil mass on the main kinetic parameters. Activation energy was 0.6–64 × 10³ kJ mol^?1, with higher variation in Test-1. LTO region was represented by just one reaction and its activation energy was ~10² kJ mol^?1 across every tests. Process variables were found to affect the exothermal temperature interval, the activation energy, and the order of reaction. Effects of variables on the kinetic parameters were found to be dependent on specific reaction temperature range, being more pronounced in the range of higher temperatures.     

A new method for asperphenamate synthesis and its antimicrobial activity evaluation

Asperphenamate is a natural phenylalanine derivative. This compound was produced through a new, two-step synthetic route. It was also evaluated by the antimicrobial activity of the pure substance against Escherichia coli, Staphylococcus aureus and Cladosporium herbarum.     

Rapidity dependence of multiplicity distributions in proton-nucleus collisions at 360 GeV/c

Multiplicity distributions in various rapidity intervals for charged particles produced in collisions of 360 GeV/c protons with aluminium (Al) and gold (Au) targets are presented. The data were analysed separately for the forward and backward hemispheres. Each distribution is well described by a negative binomial distribution. The experimental distributions are compared with the predictions of the multichain model calculated by the Monte Carlo program MCMHA in which the intranuclear cascade process is included, and also with the Lund Monte Carlo FRITIOF. The results of MCMHA reproduce quite well the multiplicity distributions for various rapidity intervals.